Fig. 2.

Multidimensional scaling analysis (MDS) of the identity-by-state (IBS) similarity matrix. Top left: each strain is plotted in the 2 main dimensions of the MDS configuration. The distance between each dot represents the genetic distance of any given 2 strains. Notice the 2 main clusters: an SHR cluster (●) and a WKY cluster (■). However, the WKY/Gla substrain was intermediate between the SHR and WKY clusters. The German WKY/NCrl strain deviated far from the SHR and WKY clusters as did the outbred SD strain. Top right: MDS configuration with the inclusion of the 3rd dimension. The graph plots each strain in dimensions 2 and 3, showing the differences between the German WKY/NCrl and the SD rats in dimension 3. Bottom left: Shepard diagram for the 2-dimensional configuration. The y-axis is the calculated distance between any 2 strains in the MDS solutions. The x-axis is the actual genetic disparities between the 2. Most of the dots fall in the diagonal line, meaning that the genetic distances in the MDS solutions provides a good prediction to the actual genetic disparities. One exception is shown as the black dot which represents the German WKY/NCrl comparison with the SD on the 2-dimensional MDS plot. Among all the 2×2 comparisons, the differences between the SD strain and all other strains, except the German WKY/NCrl rats, are the largest (green dots), whereas the differences between German WKY/NCrl rats with all other rats, except the SD rats, are the 2nd largest (red dots). All other 2×2 strain comparisons showed less distance and are plotted in blue. Bottom right: Shepard diagram for the 3-dimensional configuration, showing an improved fit for the German WKY/NCrl and SD rats comparisons.