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 χ2 distribution to yield the associated P values. ∆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 two-, three-, and four-way interactions among the variables. Consequently the LRT and P values for dropping single terms cannot be calculated.

Model 1Model 2Model 3Model 4
LRT−log10(P)LRT−log10(P)LRT−log10(P)LRT−log10(P)
Gene size14933.538.79.30XX
RNAi13.13.510.83.00XX
Conservation222.649.681.618.77XX
Distant linkage36.28.735.18.51XX
Interaction termsXX
Recombination rate
Chromosomal domain263.157.12444.896.59
Background selection
Explained deviance337.8600.9444.8370.6
Residual deviance12,559.712,296.612,452.712,526.9
∆df46215
AIC12,569.712,310.612,458.712,558.9
Model 5Model 6Model 7Model 8
LRT−log10(P)LRT−log10(P)LRT−log10(P)LRT−log10(P)
Gene size121.927.6238.49.2322.65.7122.55.68
RNAi14.43.8311.13.0611.83.2311.93.25
Conservation193.638.9481.618.7844.210.544410.49
Distant linkage35.98.6835.18.5033.48.1233.38.11
Interaction terms
Recombination rate52.112.271.20.56
Chromosomal domain212.246.070.30.06
Background selection363.680.32100.722.98
Explained deviance389.9602.1701.4701.6
Residual deviance12,507.612,295.412,196.112,195.9
∆df5757
AIC12,519.612,311.412,208.112,211.9