Table 1.
Estimation of selection acting on gene methylation state on the Salk dataset
| Gene number | Mean 4.Ne.s | 4.Ne.s credible interval | Conclusion | ||
|---|---|---|---|---|---|
| All genes | 22,609 | 4.Ne.sUM = 0.064 | 0.011–0.127 | No selection on gene methylation (4.Ne.s ≪ 1) | |
| Ancestrally gbM genes | 3,243 | 4.Ne.sgbM = 1.637 | 1.359–1.896 | gbM state advantageous (4.Ne.sgbM ≫ 1) | |
| Ancestrally UM genes | 7,626 | 4.Ne.sUM = 1.896 | 1.514–2.237 | UM state advantageous (4.Ne.sUM ≫ 1) | |
| CHG-gain orthologs | 7,534 | 4.Ne.sgbM = 0.286 | 0.176–0.393 | No selection on gene methylation (4.Ne.s ≪ 1) | |
| No-CHG-gain orthologs | 15,093 | 4.Ne.sUM = 0.355 | 0.246–0.468 | No selection on gene methylation (4.Ne.s ≪ 1) | |
| Ancestrally gbM | CHG-gain orthologs | 1,984 | 4.Ne.sgbM = 1.623 | 1.337–1.910 | gbM state advantageous (4.Ne.sgbM ≫ 1) |
| no-CHG-gain orthologs | 1,250 | 4.Ne.sgbM = 1.637 | 1.266–2.005 | gbM state advantageous (4.Ne.sgbM ≫ 1) | |
| Ancestrally UM | CHG-gain orthologs | 2,184 | 4.Ne.sUM = 3.437 | 2.905–3.915 | UM state advantageous (4.Ne.sUM ≫ 1) |
| no-CHG-gain orthologs | 5,349 | 4.Ne.sUM = 3.178 | 2.728–3.601 | UM state advantageous (4.Ne.sUM ≫ 1) | |
Parameters of the SFS model were estimated using an mcmc approach (see Materials and Methods for details). The estimated mean selection efficacy (either 4.Ne.sUM or 4.Ne.sgbM, depending on which is higher) is shown and its 95% credible interval. If 4.Ne.s > 1.0 and if 1.0 is not included in the credible interval, then significant selection is inferred to act on methylation state (either the UM or the gbM state is advantageous). Details on inferred values of other parameters of the model can be found in Supplementary Table S2. These results come from one mcmc run and are equivalent to results obtained from two independent runs with random parameter initiation values (Supplementary Table S2).