Figure 1. Genetic, Sequence, and Morphological Evidence for Dual Loci Controlling Armor Plate Dimensions in Sticklebacks.

(A) Two distinct, but closely-linked loci regulate armor plate height and width. Plate height (green) and width (red) were mapped in a large marine x benthic F2 cross using MapQTL. Likelihood-of-odds (LOD) scores and the percent variance explained (PVE) for peak markers for each trait are shown. The 2-LOD intervals for each QTL are shaded (green and red, overlap in yellow), and high significance cut offs (1000 permutations with MapQTL; p<0.001) are shown with dotted lines. Representative fish from the grandparental marine and benthic populations stained with Alizarin red are shown.

(B) There are two major peaks of repeated sequence divergence between freshwater and marine fish in the plate size interval. Sequence divergence between pairs (n=11) of geographically proximal marine and freshwater sticklebacks are plotted (colored lines). Populations are listed in Table S2. The 2-LOD score intervals for plate height and width (black rectangles), the GDF6 locus, and the region cloned for testing for enhancer activity in Figure 2 are shown.

(C and D) Geographic patterns in armor plate morphology match patterns of sequence divergence. Armor plate height (C) and width (D) were measured from adults (Table S2) from each of the twenty-one sequenced populations and were normalized for standard fish depth and length, respectively. Pacific basin freshwater (FW) populations are shown in black, Atlantic basin freshwater populations in gray, and Pacific and Atlantic basin marine populations in white. Two-sample Wilcoxon tests were used to examine the significances of plate size averages distribution differences between groups of fish populations (bracketed), and p-values are shown. Error bars represent SEM.

See also Figure S1 and Tables S1, S2 and S3.