(A) The mean distances between genes vs. the genomic distance for when both genes were (0,0),(1,1), (0,1), and the mean distances between loci not containing the investigated genes. Boxplots show quartiles and whiskers expand to 1.5× interquartile range, black diamonds are outliers. (B) The difference between the scenarios shown in (A), showing the difference in mean distance on a gene pair by gene pair basis, and a black line is shown to aid in visualization of zero. (C) The same analysis as in (B) but vs. the median physical distance (MPD) between the genes. (D–G) The difference shown in (B) and (C) but vs. either the MPD minus the expected MPD or the genomic distance minus the expected genomic distance (see text). Boxplots show quartiles and whiskers expand to 1.5× interquartile range, black diamonds are outliers. Black lines and dots are means and error bars are SEM from bootstrapping (Appendix 1). Significance was defined as a p-value < 0.01 with a t-test (Appendix 1).