Fig. 4: Long-distance linkage disequilibrium and ILD among the four candidate intervals.
From: Inter-chromosomal coupling between vision and pigmentation genes during genomic divergence
a, The four intervals displayed islands of increased linkage disequilibrium. b, Genome-wide ILD. Box edges represent the 25th and 75th percentiles, whiskers show 1.5× the interquartile range, dots are outliers, and red lines represent the r2 expectation for the mean (1/2n, where n is the sample size). Genome-wide ILD was lower for the global dataset due to the larger sample size (n = 110) compared with the location- and species-specific datasets (n = 35–39). c, ILD among the four candidate intervals. d, Linkage disequilibrium among the four intervals increased with increasing differentiation among species (grey gradient). e, In contrast, linkage disequilibrium among the four intervals was low or absent within species. r2 values are shown on a SNP basis in b and c and averaged over two-dimensional bins of 10 × 10 kb in a,d and e.
