Table 2. SNPs of particular biological interest.
For selected SNPs in the mixed-population samples, the negative base–10 logarithm of the E-value, maximum-likelihood prediction of the frequency of the derived allele in the population, and gene (e.g., araJ) or intergenic region (e.g., rspA/ynfA) containing the SNP are shown. Samples where the same mutation was fixed (within statistical resolution) in a mixed-population sample (M) or present in a sequenced clone (C) at a given generation are marked in the notes column, with a plus sign further indicating that the mutation was also found in all later samples, and asterisks marking a few SNPs that appeared (erroneously, owing to statistical uncertainty) to have been fixed in earlier population samples. Other mutations are likely to be beneficial because they are in the same gene or promoter region as mutations that later swept to fixation in this population (new allele), probably affect cellular processes known to be targets of selection in this experiment (cell wall, respiration, ribosome, regulation), or possibly improve growth on metabolic byproducts (acetate, SCFA). A complete list of all predicted SNPs that includes further details is available on the author's website (https://myxo.css.msu.edu/papers/)
| −log10 E | Freq | Gene | Notes |
|---|---|---|---|
| 2K mixed-population sample | |||
| 16.7 | 10.0% | mrdB | cell wall |
| 12.2 | 12.8% | mreB | cell wall |
| 12.2 | 14.8% | yegI | M5K+ C5K+ |
| 6.4 | 6.9% | pykF | new allele |
| 4.2 | 10.1% | hslU | M5K+ C5K+ |
| 0.6 | 4.4% | iclR | new allele |
| 5K mixed-population sample | |||
| 5.1 | 94.4% | infB | M10K+ C5K+ |
| 3.9 | 92.9% | malT | M10K+ C5K+ |
| 2.5 | 6.8% | atoC | SCFA |
| 1.7 | 94.9% | spoT | *M2K+ C2K+ |
| 10K mixed-population sample | |||
| 80.8 | 45.6% | yghJ | M20K+ C10K+ |
| 77.0 | 33.1% | hsdM | C10K |
| 72.8 | 61.6% | rpsM | M20K+ C10K+ |
| 69.9 | 43.2% | araJ | M20K+ C10K+ |
| 65.2 | 53.8% | yhdG/fis | M20K+ C10K+ |
| 64.4 | 34.1% | acs/nrfA | acetate |
| 60.1 | 57.3% | rpsA | ribosome |
| 49.0 | 39.0% | yedW/yedX | M20K+ C10K+ |
| 44.3 | 33.1% | maeB/talA | C10K |
| 23.4 | 16.2% | nuoM | respiration |
| 20.7 | 13.6% | nuoG | respiration |
| 20.3 | 23.0% | elaD | synonymous |
| 4.9 | 9.8% | ompF/asnS | new allele |
| 3.8 | 8.1% | nadR | M15K+ C15K+ |
| 3.8 | 10.3% | ompF/asnS | new allele |
| 3.4 | 9.8% | iclR/metH | new allele |
| 2.9 | 8.7% | leuO/ilvI | regulation |
| 2.3 | 5.5% | atoS | SCFA |
| 15K mixed-population sample | |||
| 31.3 | 82.8% | iclR | M20K+ C15K+ |
| 10.5 | 90.6% | rpsM | M20K+ C10K+ |
| 6.8 | 91.2% | pcnB | M20K+ C15K+ |
| 5.2 | 90.3% | arcB | M20K+ C15K+ |
| 4.8 | 94.7% | infB | *M10K+ C5K+ |
| 4.6 | 91.9% | dhaM | M20K+ C15K+ |
| 4.0 | 94.5% | araJ | M20K+ C10K+ |
| 3.9 | 91.3% | narI/ychS | M20K+ C15K+ |
| 2.3 | 4.1% | yaaH | acetate |
| 2.1 | 95.8% | yghJ | M20K+ C10K+ |
| 2.0 | 7.7% | ydiV/nlpC | regulation |
| 1.8 | 91.2% | ompF/asnS | M20K+ C15K+ |
| 1.8 | 7.6% | ycbX/ycbY | ribosome |
| 1.1 | 93.9% | yhdG/fis | M20K+ C10K+ |
| 1.0 | 95.9% | yedW/yedX | M20K+ C10K+ |
| 0.8 | 5.9% | gyrB | regulation |
| 0.6 | 95.2% | yegI | *M5K+ C5K+ |
| 0.4 | 4.6% | rspA/ynfA | regulation |
| 0.0 | 95.6% | ebgR | M20K+ C15K+ |
| 20K mixed-population sample | |||
| 40.0 | 35.3% | hypF | C20K+ |
| 1.3 | 5.6% | mgrB/yobH | regulation |