Figure 4

Gene retrocopy insertions in mice. (a) Number of gene retrocopies absent from the C57BL/6J reference (y-axis) present in each of 17 inbred mouse strains [47] (x-axis). (b) Heatmap created by the heatmap.2 function in the gplots package in R based on the Jaccard distance from pairwise comparison of GRIP alleles between strains (Materials and methods). C57BL/6NJ was left out of the inter-strain comparison of non-reference GRIPs because all but one insertion was shared with the C57BL/6J reference. As indicated on the histogram to the left of the heatmap, distances range from 0 (white, GRIP profile) to 1 (dark blue, no overlap in GRIP profiles). Hierarchical clustering of similarity indices generally recapitulates the breeding history of wild and inbred mouse strains [50].