Table 2.
Logistic regression models implicate mutation, stabilizing selection, and linked selection in explaining the distribution of local linkages.
LRT: likelihood ratio test statistic comparing the logistic regression model in which the specified term has been dropped to the model in which all terms are included. LRT is equivalent to the drop in explained deviance due to excluding the term from the model. The null deviance is 12897.5. The LRT was tested against a chi-square distribution to yield the associated p-values. Δ df: difference in degrees of freedom between the specified model and the null model including only the intercept. Chromosomal domain is a factor with three levels and hence contributes two degrees of freedom. AIC Akaike information criterion. Model 4 includes all 2-, 3-, and 4-way interactions among the variables. Consequently the LRT and p-values for dropping single terms cannot be calculated.
| MODEL 1 | MODEL 2 | MODEL 3 | MODEL 4 | |||||
|---|---|---|---|---|---|---|---|---|
| LRT | −log10(p) | LRT | −log10(p) | LRT | −log10(p) | LRT | −log10(p) | |
| gene size | 149 | 33.5 | 38.7 | 9.30 | X | X | ||
| RNAi | 13.1 | 3.5 | 10.8 | 3.00 | X | X | ||
| Conservation | 222.6 | 49.6 | 81.6 | 18.77 | X | X | ||
| distant linkage | 36.2 | 8.7 | 35.1 | 8.51 | X | X | ||
| interaction terms | X | X | ||||||
| recombination rate | ||||||||
| chromosomal domain | 263.1 | 57.12 | 444.8 | 96.59 | ||||
| background selection | ||||||||
| explained deviance | 337.8 | 600.9 | 444.8 | 370.6 | ||||
| residual deviance | 12559.7 | 12296.6 | 12452.7 | 12526.9 | ||||
| Δ df | 4 | 6 | 2 | 15 | ||||
| AIC | 12569.7 | 12310.6 | 12458.7 | 12558.9 | ||||
| MODEL 5 | MODEL 6 | MODEL 7 | MODEL 8 | |||||
| LRT | −log10(p) | LRT | −log10(p) | LRT | −log10(p) | LRT | −log10(p) | |
| gene size | 121.9 | 27.62 | 38.4 | 9.23 | 22.6 | 5.71 | 22.5 | 5.68 |
| RNAi | 14.4 | 3.83 | 11.1 | 3.06 | 11.8 | 3.23 | 11.9 | 3.25 |
| Conservation | 193.6 | 38.94 | 81.6 | 18.78 | 44.2 | 10.54 | 44 | 10.49 |
| distant linkage | 35.9 | 8.68 | 35.1 | 8.50 | 33.4 | 8.12 | 33.3 | 8.11 |
| interaction terms | ||||||||
| recombination rate | 52.1 | 12.27 | 1.2 | 0.56 | ||||
| chromosomal domain | 212.2 | 46.07 | 0.3 | 0.06 | ||||
| background selection | 363.6 | 80.32 | 100.7 | 22.98 | ||||
| explained deviance | 389.9 | 602.1 | 701.4 | 701.6 | ||||
| residual deviance | 12507.6 | 12295.4 | 12196.1 | 12195.9 | ||||
| Δ df | 5 | 7 | 5 | 7 | ||||
| AIC | 12519.6 | 12311.4 | 12208.1 | 12211.9 | ||||