Table 1 Type I error rates for all runs in our 23 experimental design. We set (marginal) genetic variances (i.e., diagonal elements of Embedded Image) to 1 in all runs. Embedded Image was set to the 2 by 2 identity matrix in all runs. We used allele probabilities at a single genetic marker to simulate traits for all eight sets of parameter inputs. In the column “Allele effects partitioning”, “ABCD:EFGH” means that lines A–D carry one QTL allele while lines E–H carry the other allele. “F:ABCDEGH” means the QTL has a private allele in strain F
RunΔ(Allele effects)Allele effects partitioningGenetic correlationType I error rate
16ABCD:EFGH00.032
26ABCD:EFGH0.60.035
36F:ABCDEGH00.040
46F:ABCDEGH0.60.045
512ABCD:EFGH00.038
612ABCD:EFGH0.60.042
712F:ABCDEGH00.025
812F:ABCDEGH0.60.025