Appendix 1—table 2. Path sampling results and model selection based on Δ marginal L estimates (relative to best model (ref)) considering 75 path sampling steps and chain lengths of 15 million.
Comparisons of Beast runs using a combined dataset of Central Asian outbreak (CAO) isolates originated from Germany (1995 – 2000), Karakalpakstan (2001–2006), and Samara (2008 – 2010) as well as comparisons of Beast runs from CAO-Karakalpakstan data employing the best clock model/substitution rate estimate and runs with the 95% HPD intervals for the substitution rate. Mean node age of CAO-MRCA and acquisition of putative compensatory mutation rpoC N698S of CAO-Karakalpakstan clade are given for each model.
| Clock model | Demographic model | Marginal L estimate | Mean ESS |
Δ marginal L estimate | Subst rate x 10−7 (95%HPD) | MRCA and rpoC N698S mean node age (95%HPD) |
|---|---|---|---|---|---|---|
| Combined CAO dataset for clock model comparison | ||||||
| Strict (no tip dating) |
Coalescent constant size | −10131.67 | 4302 | 32.21 | 1.0 (fixed) |
41.5 (30.6–49.1) NA |
| Strict (tip dating) |
Coalescent constant size | −10099.46 | 4041 | ref | 1.0 (fixed) |
42.9 (34.3–50.3) NA |
| Relaxed, lognormal | Coalescent constant size | −10117.21 | 1303 | 17.75 | 0.96 (0.65–1.24) |
57.6 (34.4–84.5) NA |
| Combined CAO dataset for molecular clock estimate among CAO strains | ||||||
| Relaxed, lognormal | Coalescent constant size | −10117.21 | 1303 | 78.28 | 0.96 (0.65–1.24) |
57.6 (34.4–84.5) NA |
| Relaxed, lognormal | Exponential | −10044.41 | 1266 | 5.48 | 0.88 (0.58–1.21) |
40.5 (26.4–53.2) NA |
| Relaxed, lognormal | Bayesian skyline | −10038.93 | 924 | ref | 0.94 (0.72–1.15) |
37.1 (25.7–44.0) NA |
| CAO-Karakalpakstan dataset for demographic model comparison (under best clock estimate) | ||||||
| Strict (tip dating) |
Bayesian skyline | −7617.09 | 2874 | 3.79 | 0.94 (fixed) |
32.2 (23.9–37.3) 16.1 (11.6–16.9) |
| Strict (tip dating) |
Coalescent constant size | −7667.92 | 4231 | 54.62 | 0.94 (fixed) |
37.5 (30.2–45.1) 15.8 (12.3–18.6) |
| Strict (tip dating) |
Exponential | −7613.30 | 4003 | ref | 0.94 (fixed) |
29.3 (23.5–33.7) 15.4 (12.4–20.1) |
| CAO-Karakalpakstan dataset, exponential growth model, upper and lower 95% HPD values (from best clock estimate) | ||||||
| Strict (tip dating) |
Exponential | −7610.94 | 3926 | ref | 0.72 (fixed) |
36.4 (30.4–43.3) 18.4 (15.8–21.6) |
| Strict (tip dating) |
Exponential | −7613.30 | 4003 | 2.36 | 0.94 (fixed) |
29.3 (23.5–33.7) 15.4 (12.4–20.1) |
| Strict (tip dating) |
Exponential | −7621.22 | 4031 | 10.28 | 1.15 (fixed) |
24.4 (20.0–25.8) 12.9 (10.8–14.4) |
| CAO-Karakalpakstan dataset, skyline model, upper and lower 95% HPD values (from best clock estimate) | ||||||
| Strict (tip dating) |
Bayesian skyline | −7611.12 | 2694 | ref | 0.72 (fixed) |
39.5 (30.7–47.8) 18.8 (14.6–21.5) |
| Strict (tip dating) |
Bayesian skyline | −7617.09 | 2874 | 5.97 | 0.94 (fixed) |
32.2 (23.9–37.3) 16.1 (11.6–16.9) |
| Strict (tip dating) |
Bayesian skyline | −7619.71 | 2763 | 8.59 | 1.15 (fixed) |
25.2 (20.2–30.7) 11.8 (10.1–13.9) |
Abbreviations: HPD = Highest posterior density interval.