Table 2.
Selection of demographic models for the Bayesian phylogenetic analysis of the CVB5 1DVP1 genea
| Parameter | Genogroup A (n = 126) |
Genogroup B (n = 169) |
||||||
|---|---|---|---|---|---|---|---|---|
| Marginal likelihood |
tMRCA (calendar yr) | Mean substitution rate (10−3 substitutions/site/yr) | Marginal likelihood |
tMRCA (calendar yr) | Mean substitution rate (10−3 substitution/site/yr) | |||
| PSb | SSc | PS | SS | |||||
| BSP | −8,627.8152 | −8,628.3069 | 1908 (1849–1948) | 5.449 (3.69–7.367) | −11,049.2201 | −11,050.0717 | 1941 (1912–1962) | 5.613 (4.54–6.615) |
| GMRF/BS | −8,682.8956 | −8,683.7626 | 1949 (1944–1952) | 7.307 (6.097–8.56) | −11,087.8397 | −11,088.8417 | 1963 (1959–1966) | 6.159 (5.383–6.968) |
| BD/SS | −8,690.9063 | −8,691.4030 | 1951 (1950–1952) | 9.054 (7.748–10.428) | −11,087.1253 | −11,087.8962 | 1964 (1962–1966) | 7.106 (6.182–8.024) |
| BD/BRN | −8,697.4840 | −8,697.9942 | 1951 (1950–1952) | 9.059 (7.784–10.438) | −11,091.9033 | −11,092.6482 | 1964.5 (1962–1966) | 7.212 (6.313–8.213) |
a
The phylogenetic reconstructions were done with the SRD06 substitution model and an uncorrelated relaxed clock model including an underlying exponential distribution with the BEAST (v1.7.5) program. Abbreviations: n, number of sequences; BSP, Bayesian skyline plot; GMRF/BS, Gaussian Markov random fields Bayesian skyride; BD/SS, birth-death serial sampling; BD/BRN, birth-death basic reproduction number. Years in parentheses are 95% HPD intervals.
b
The log marginal-likelihood estimate was calculated with the path sampling (PS) method.
c
The log marginal-likelihood estimate was calculated with the stepping-stone (SS) method.