From: Differential strengths of selection on S-RNases from Physalis and Solanum(Solanaceae)
HA: Rates free to vary | |||||||
---|---|---|---|---|---|---|---|
Log likelihood: -16749.63 | Parameters: 229 | ||||||
Inferred rates for Physalis: | Inferred rates for Solanum: | ||||||
dN/dS | dS | dN | Prob | dN/dS | dS | dN | Prob |
2.663 | 1.047 | 2.788 | 0.463 | 1.139 | 0.942 | 1.073 | 0.353 |
1.000 | 0.814 | 0.814 | 0.311 | 1.000 | 2.000 | 2.000 | 0.094 |
0.000 | 0.580 | 0.000 | 0.081 | 0.496 | 0.800 | 0.397 | 0.274 |
0.177 | 1.487 | 0.262 | 0.144 | 0.083 | 0.933 | 0.077 | 0.279 |
a) H 0 : Same strength of selection | Â | ||||||
Log likelihood: -16765.49 | Parameters: 228 | ||||||
Inferred rates for Physalis: | Inferred rates for Solanum: | ||||||
dN/dS | dS | dN | Prob | dN/dS | dS | dN | Prob |
1.664 | 1.261 | 2.099 | 0.466 | 1.664 | 0.781 | 1.300 | 0.337 |
1.000 | 0.647 | 0.647 | 0.312 | 1.000 | 2.241 | 2.241 | 0.086 |
0.000 | 0.470 | 0.000 | 0.081 | 0.527 | 0.884 | 0.466 | 0.290 |
0.171 | 1.222 | 0.209 | 0.141 | 0.087 | 1.001 | 0.087 | 0.286 |
Are selection strengths (dN/dS) different? | |||||||
LRT = 31.722 p < 0.0001; DF = 1 | |||||||
b) H 0 : Same proportion of selected sites | |||||||
Log likelihood: -16750.60 | Parameters: 228 | ||||||
Inferred rates for Physalis: | Inferred rates for Solanum: | ||||||
dN/dS | dS | dN | Prob | dN/dS | dS | dN | Prob |
2.737 | 1.042 | 2.851 | 0.397 | 1.143 | 0.949 | 1.085 | 0.397 |
1.000 | 0.900 | 0.900 | 0.339 | 1.000 | 2.065 | 2.065 | 0.081 |
0.000 | 0.573 | 0.000 | 0.084 | 0.491 | 0.804 | 0.395 | 0.258 |
0.216 | 1.297 | 0.280 | 0.180 | 0.082 | 0.939 | 0.077 | 0.264 |
Are the proportions of codons under selection different? | |||||||
LRT = 1.929 p < 0.165; DF = 1 | |||||||
c) H 0 : Same dN/dS and proportions | |||||||
Log likelihood: -16766.96 | Parameters: 228 | ||||||
Inferred rates for Physalis: | Inferred rates for Solanum: | ||||||
dN/dS | dS | dN | Prob | dN/dS | dS | dN | Prob |
1.636 | 1.318 | 2.157 | 0.397 | 1.636 | 0.805 | 1.318 | 0.397 |
1.000 | 0.703 | 0.703 | 0.348 | 1.000 | 2.341 | 2.341 | 0.074 |
0.000 | 0.472 | 0.000 | 0.087 | 0.517 | 0.894 | 0.463 | 0.265 |
0.193 | 1.136 | 0.219 | 0.169 | 0.086 | 1.022 | 0.088 | 0.264 |
Are selective regimes (dN/dS and proportions) different? | |||||||
LRT = 34.647 p < 0.0001; DF = 2 | |||||||
d) H 0 : Shared distributions of rates | |||||||
Log likelihood: -16764.30 | Parameters: 219 | ||||||
Inferred joint rates: | Â | Â | Â | Â | |||
dN/dS | dS | dN | Prob | Â | Â | Â | Â |
2.507 | 1.034 | 2.593 | 0.189 | Â | Â | Â | Â |
1.000 | 1.139 | 1.139 | 0.338 | Â | Â | Â | Â |
0.543 | 0.797 | 0.433 | 0.251 | Â | Â | Â | Â |
0.086 | 0.988 | 0.085 | 0.222 | Â | Â | Â | Â |
Are the distributions different? | |||||||
LRT = 29.350 p < 0.001; DF = 10 |