Table 4. Branch-site model tests for adaptive evolution among codon sites for the foreground HLII branch.
Background lineages include Synechococcus and all other Prochlorococcus. Bolded LRT statistic values are chi-square critical values that meet a significance level of <0.001 with 1 degree of freedom.
Table 4—source data 1. Compressed tar archive (zip format) containing example codeml control files, codon alignments (phylip format), and tree files (newick format) used for branch-site model tests of adaptive evolution in the HLII clade.
elife-41043-table4-data1.zip (484.9KB, zip)
DOI: 10.7554/eLife.41043.025
| Gene | Hypothesis log-likelihood | Site class 0 | Site class 1 | Site class 2a | Site class 2b | LRT statistic | |
|---|---|---|---|---|---|---|---|
| gyrB | H0 −104105 |
proportion of sites | 0.98759 | 0.00138 | 0.01102 | 0.00002 | 6074 |
| background dN/dS | 0 | 1 | 0 | 1 | |||
| foreground dN/dS | 0 | 1 | 1 | 1 | |||
| H1 −101068 |
proportion of sites | 0.99666 | 0.00177 | 0.00157 | 0 | ||
| background dN/dS | 0.00908 | 1 | 0.00908 | 1 | |||
| foreground dN/dS | 0.00908 | 1 | 1 | 1 | |||
| pstB | H0 −39463 |
proportion of sites | 0.99801 | 0.00161 | 0.00038 | 0 | 0 |
| background dN/dS | 0.03255 | 1 | 0.03255 | 1 | |||
| foreground dN/dS | 0.03255 | 1 | 1 | 1 | |||
| H1 −39463 |
proportion of sites | 0.99801 | 0.00161 | 0.00038 | 0 | ||
| background dN/dS | 0.03255 | 1 | 0.03255 | 1 | |||
| foreground dN/dS | 0.03255 | 1 | 1 | 1 | |||
| amtB | H0 −68231 |
proportion of sites | 0.9926 | 0.00663 | 0.00076 | 0.00001 | -2 |
| background dN/dS | 0.02052 | 1 | 0.02052 | 1 | |||
| foreground dN/dS | 0.02052 | 1 | 1 | 1 | |||
| H1 −68232 |
proportion of sites | 0.99288 | 0.00657 | 0.00054 | 0 | ||
| background dN/dS | 0.0206 | 1 | 0.0206 | 1 | |||
| foreground dN/dS | 0.0206 | 1 | 2.17216 | 2.17216 | |||
| glnA | H0 −65896 |
proportion of sites | 0.99839 | 0.00144 | 0.00018 | 0 | 0 |
| background dN/dS | 0.01722 | 1 | 0.01722 | 1 | |||
| foreground dN/dS | 0.01722 | 1 | 1 | 1 | |||
| H1 −65896 |
proportion of sites | 0.99839 | 0.00144 | 0.00018 | 0 | ||
| background dN/dS | 0.01722 | 1 | 0.01722 | 1 | |||
| foreground dN/dS | 0.01722 | 1 | 1 | 1 | |||
| glsF | H0 −249282 |
proportion of sites | 0.99092 | 0.00679 | 0.00227 | 0.00002 | 0 |
| background dN/dS | 0.0227 | 1 | 0.0227 | 1 | |||
| foreground dN/dS | 0.0227 | 1 | 1 | 1 | |||
| H1 −249282 |
proportion of sites | 0.99092 | 0.00679 | 0.00227 | 0.00002 | ||
| background dN/dS | 0.0227 | 1 | 0.0227 | 1 | |||
| foreground dN/dS | 0.0227 | 1 | 1 | 1 | |||
| napA | H0 −23009 |
proportion of sites | 0.97966 | 0.01219 | 0.00805 | 0.0001 | 0 |
| background dN/dS | 0.00928 | 1 | 0.00928 | 1 | |||
| foreground dN/dS | 0.00928 | 1 | 1 | 1 | |||
| H1 −23009 |
proportion of sites | 0.97966 | 0.01219 | 0.00805 | 0.0001 | ||
| background dN/dS | 0.00928 | 1 | 0.00928 | 1 | |||
| foreground dN/dS | 0.00928 | 1 | 1 | 1 | |||
| narB | H0 −38711 |
proportion of sites | 0.94311 | 0.02164 | 0.03446 | 0.00079 | 0 |
| background dN/dS | 0.02489 | 1 | 0.02489 | 1 | |||
| foreground dN/dS | 0.02489 | 1 | 1 | 1 | |||
| H1 −38711 |
proportion of sites | 0.94311 | 0.02164 | 0.03447 | 0.00079 | ||
| background dN/dS | 0.02489 | 1 | 0.02489 | 1 | |||
| foreground dN/dS | 0.02489 | 1 | 1 | 1 | |||
| moaA | H0 −22958 |
proportion of sites | 0.94068 | 0.03375 | 0.02468 | 0.00089 | 0 |
| background dN/dS | 0.03882 | 1 | 0.03882 | 1 | |||
| foreground dN/dS | 0.03882 | 1 | 1 | 1 | |||
| H1 −22958 |
proportion of sites | 0.94068 | 0.03375 | 0.02468 | 0.00089 | ||
| background dN/dS | 0.03882 | 1 | 0.03882 | 1 | |||
| foreground dN/dS | 0.03882 | 1 | 1 | 1 | |||
| nirA | H0 −52348 |
proportion | 0.97996 | 0.01302 | 0.00693 | 0.00009 | 14 |
| background dN/dS | 0.04327 | 1 | 0.04327 | 1 | |||
| foreground dN/dS | 0.04327 | 1 | 1 | 1 | |||
| H1 −52341 |
proportion | 0.97254 | 0.0124 | 0.01487 | 0.00019 | ||
| background dN/dS | 0.04293 | 1 | 0.04293 | 1 | |||
| foreground dN/dS | 0.04293 | 1 | 1 | 1 |