Best fit QTL models for different numbers of QTL for the D. santomea and D. yakuba backcrosses.

†For the D. santomea backcross, this is the effect of introducing one D. yakuba allele of the specified QTL, and vice versa for the D. yakuba backcross.‡Log likelihood ratios comparing the full model to a model with the specified QTL removed.§This alternative four QTL model for the D. santomea backcross did not have a substantially lower LOD score than the best-fit four QTL model, suggesting that it is not possible to differentiate between a QTL at ∼15.7 Mb and at ∼29 Mb on chromosome 2.**An alternative two QTL models with one QTL at ∼15.7 had LOD scores at least 0.76 LOD lower than the best-fit model.