Table 1

Model Selection Analysis Results

Data set

Molecular clock model

Coalescent Modela

Marginal Log Likelihood

Genomic rate of evolutionb(×10-3subs./site/year)

Relaxed clock coefficient of variation

Relative rate of evolution (codon positions 1 & 2)

Relative rate of evolution (codon position 3)


Among-host (1a)

Strict

Constant

-90901.35

1.30 (1.16 - 1.43)

Not applicable

0.72 (0.70 - 0.74)

1.56 (1.51 - 1.60)

Relaxed

Constant

-90632.03

1.44 (1.00 - 1.84)

0.25 (0.21 - 0.30)

0.72 (0.70 - 0.74)

1.56 (1.51 - 1.60)

Relaxed

Expo

-90632.39

1.47 (1.02 - 1.87)

0.24 (0.20 - 0.29)

0.72 (0.70 - 0.74)

1.56 (1.51 - 1.60)

Relaxed

BSP

-90632.49

1.48 (1.09 - 1.84)

0.23 (0.20 - 0.27)

0.72 (0.70 - 0.75)

1.55 (1.51 - 1.60)


Among-host (1b)

Strict

Constant

-88288.70

1.04 (0.87 - 1.22)

Not applicable

0.66 (0.64 - 0.68)

1.68 (1.63 - 1.72)

Relaxed

Constant

-88127.66

1.25 (0.73 - 1.73)

0.22 (0.18 - 0.26)

0.66 (0.64 - 0.68)

1.68 (1.64 - 1.72)

Relaxed

Expo

-88125.80

1.24 (0.75 - 1.74)

0.21 (0.17 - 0.25)

0.66 (0.64 - 0.68)

1.68 (1.64 - 1.72)

Relaxed

BSP

-88127.55

1.18 (0.67 - 1.65)

0.21 (0.17 - 0.25)

0.66 (0.64 - 0.68)

1.68 (1.63 - 1.72)


Within-host

Strict

Constant

-31070.20

1.12 (1.02 - 1.23)

Not applicable

0.58 (0.54 - 0.61)

1.85 (1.78 - 1.92)

Relaxed

Constant

-31013.86

1.11 (0.97 - 1.23)

0.27 (0.19 - 0.37)

0.58 (0.54 - 0.61)

1.85 (1.78 - 1.92)

Relaxed

Expo

-31013.56

1.13 (1.01 - 1.27)

0.30 (0.19 - 0.42)

0.58 (0.54 - 0.61)

1.85 (1.78 - 1.92)

Relaxed

BSP

-31012.14

1.11 (0.98 - 1.24)

0.27 (0.19 - 0.34)

0.58 (0.54 - 0.61)

1.85 (1.78 - 1.92)


a Constant = constant population size, Expo = exponential growth, BSP = Bayesian skyline plot

b A single average rate of evolution estimated across the whole genome (no partitions)

Gray et al. BMC Evolutionary Biology 2011 11:131   doi:10.1186/1471-2148-11-131

Open Data