Table 5. Branch-site model tests for adaptive evolution among codon sites for the foreground LLI 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 5—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 LLI clade.
elife-41043-table5-data1.zip (495.6KB, zip)
DOI: 10.7554/eLife.41043.027
| Gene | Hypothesis log-likelihood | Site class 0 | Site class 1 | Site class 2a | Site class 2b | LRT statistic | |
|---|---|---|---|---|---|---|---|
| gyrB | H0 −101367 |
proportion of sites | 0.99813 | 0.00187 | 0 | 0 | 22 |
| background dN/dS | 0.01062 | 1 | 0.01062 | 1 | |||
| foreground dN/dS | 0.01062 | 1 | 1 | 1 | |||
| H1 −101356 |
proportion of sites | 0.99768 | 0.00186 | 0.00046 | 0 | ||
| background dN/dS | 0.01053 | 1 | 0.01053 | 1 | |||
| foreground dN/dS | 0.01053 | 1 | 1 | 1 | |||
| pstB | H0 −39407 |
proportion of sites | 0.98046 | 0.00147 | 0.01805 | 0.00003 | 0 |
| background dN/dS | 0.03172 | 1 | 0.03172 | 1 | |||
| foreground dN/dS | 0.03172 | 1 | 1 | 1 | |||
| H1 −39407 |
proportion of sites | 0.98046 | 0.00147 | 0.01805 | 0.00003 | ||
| background dN/dS | 0.03172 | 1 | 0.03172 | 1 | |||
| foreground dN/dS | 0.03172 | 1 | 1 | 1 | |||
| amtB | H0 −68211 |
proportion of sites | 0.99157 | 0.00673 | 0.00169 | 0.00001 | 0 |
| background dN/dS | 0.01992 | 1 | 0.01992 | 1 | |||
| foreground dN/dS | 0.01992 | 1 | 1 | 1 | |||
| H1 −68211 |
proportion of sites | 0.9918 | 0.00677 | 0.00143 | 0.00001 | ||
| background dN/dS | 0.01992 | 1 | 0.01992 | 1 | |||
| foreground dN/dS | 0.01992 | 1 | 1 | 1 | |||
| glnA | H0 −65885 |
proportion of sites | 0.99799 | 0.00141 | 0.0006 | 0 | 0 |
| background dN/dS | 0.01727 | 1 | 0.01727 | 1 | |||
| foreground dN/dS | 0.01727 | 1 | 1 | 1 | |||
| H1 −65885 |
proportion of sites | 0.99799 | 0.00141 | 0.0006 | 0 | ||
| background dN/dS | 0.01727 | 1 | 0.01727 | 1 | |||
| foreground dN/dS | 0.01727 | 1 | 1 | 1 | |||
| glsF | H0 −249371 |
proportion of sites | 0.98865 | 0.00686 | 0.00445 | 0.00003 | 0 |
| background dN/dS | 0.02306 | 1 | 0.02306 | 1 | |||
| foreground dN/dS | 0.02306 | 1 | 1 | 1 | |||
| H1 −249371 |
proportion of sites | 0.98865 | 0.00686 | 0.00445 | 0.00003 | ||
| background dN/dS | 0.02306 | 1 | 0.02306 | 1 | |||
| foreground dN/dS | 0.02306 | 1 | 1 | 1 | |||
| napA | H0 −23014 |
proportion of sites | 0.97128 | 0.01248 | 0.01604 | 0.00021 | 0 |
| background dN/dS | 0.01004 | 1 | 0.01004 | 1 | |||
| foreground dN/dS | 0.01004 | 1 | 1 | 1 | |||
| H1 −23014 |
proportion of sites | 0.97122 | 0.01246 | 0.01611 | 0.00021 | ||
| background dN/dS | 0.01004 | 1 | 0.01004 | 1 | |||
| foreground dN/dS | 0.01004 | 1 | 1 | 1 | |||
| narB | H0 −38790 |
proportion of sites | 0.97596 | 0.02404 | 0 | 0 | 40 |
| background dN/dS | 0.02939 | 1 | 0.02939 | 1 | |||
| foreground dN/dS | 0.02939 | 1 | 1 | 1 | |||
| H1 −38770 |
proportion of sites | 0.9577 | 0.02346 | 0.01839 | 0.00045 | ||
| background dN/dS | 0.02762 | 1 | 0.02762 | 1 | |||
| foreground dN/dS | 0.02762 | 1 | 1 | 1 | |||
| moaA | H0 −22961 |
proportion of sites | 0.90692 | 0.03565 | 0.05526 | 0.00217 | 0 |
| background dN/dS | 0.03704 | 1 | 0.03704 | 1 | |||
| foreground dN/dS | 0.03704 | 1 | 1 | 1 | |||
| H1 −22961 |
proportion of sites | 0.90692 | 0.03565 | 0.05526 | 0.00217 | ||
| background dN/dS | 0.03704 | 1 | 0.03704 | 1 | |||
| foreground dN/dS | 0.03704 | 1 | 1 | 1 | |||
| focA | H0 −17695 |
proportion of sites | 0.97605 | 0.01411 | 0.00969 | 0.00014 | 0 |
| background dN/dS | 0.01425 | 1 | 0.01425 | 1 | |||
| foreground dN/dS | 0.01425 | 1 | 1 | 1 | |||
| H1 −17695 |
proportion of sites | 0.97605 | 0.01411 | 0.0097 | 0.00014 | ||
| background dN/dS | 0.01425 | 1 | 0.01425 | 1 | |||
| foreground dN/dS | 0.01425 | 1 | 1 | 1 | |||
| nirA type I | H0 −52349 |
proportion of sites | 0.97292 | 0.01243 | 0.01446 | 0.00018 | 0 |
| background dN/dS | 0.04333 | 1 | 0.04333 | 1 | |||
| foreground dN/dS | 0.04333 | 1 | 1 | 1 | |||
| H1 −52349 |
proportion of sites | 0.97292 | 0.01243 | 0.01446 | 0.00018 | ||
| background dN/dS | 0.04333 | 1 | 0.04333 | 1 | |||
| foreground dN/dS | 0.04333 | 1 | 1 | 1 | |||
| nirA type II | H0 −52358 |
proportion of sites | 0.97139 | 0.01216 | 0.01625 | 0.0002 | 0 |
| background dN/dS | 0.0442 | 1 | 0.0442 | 1 | |||
| foreground dN/dS | 0.0442 | 1 | 1 | 1 | |||
| H1 −52358 |
proportion of sites | 0.97139 | 0.01216 | 0.01625 | 0.0002 | ||
| background dN/dS | 0.0442 | 1 | 0.0442 | 1 | |||
| foreground dN/dS | 0.0442 | 1 | 1 | 1 |