Fig. 1: Genetic mapping, expression and role of HOXD11B in stickleback dorsal spine development.
From: Evolution of stickleback spines through independent cis-regulatory changes at HOXDB
a, Gasterosteus mapping cross. b, QTL scan results for spine number and spine length. x axis: Gasterosteus chromosomes; y axis: LOD score for three- versus four-spine trait (top), length of DS2 (bottom). The QTL peak on chromosome 6 includes the HOXDB cluster (gene diagram at the bottom, scale bar, 1 kb). The peak on chromosome 4 includes the EDA-MSX2A-STC2A cluster described elsewhere27,28. Dashed lines: genome-wide significance thresholds from permutation testing. c, Integration of GFP reporter using CRISPR–Cas9 upstream of the endogenous HOXD11B locus of low-spine Gasterosteus. Plasmid: grey; eGFP: green; basal hsp70 promoter: blue; chromosomal locus: black. Scale bar, 100 bp. TSS, transcription start site. d, eGFP expression in posterior half of fish at the stage when the dorsal spines are forming (Swarup stage 31). Scale bar, 1 mm. e, Note expression in fin fold between DS2 and DSL, DSL and dorsal fin (DF). Scale bar, 1 mm. f, X-ray of uninjected Gasterosteus (top) and Gasterosteus injected at the single-cell stage with Cas9 and sgRNA targeting the coding region of HOXD11B (bottom). Arrows: two blank pterygiophores are often located between DS2 and DSL but only in uninjected fish (insets: two blank pterygiophores in n = 5 out of 18 control and n = 0 out of 23 injected F0 mutants, two-tailed Fisher’s exact test P = 0.01). Scale bar, 5 mm. g, Length comparisons of dorsal and anal spines. Box and whisker plot: centre line, median; box limits, interquartile range (IQR); whiskers, 1.5× IQR; individual measurements shown as single points (circles: WT; triangles: mutant). y axis: residuals after accounting for standard length of fish (Extended Data Fig. 2a). DSL and AS were significantly longer in injected than uninjected fish (two-tailed t-test Bonferroni-corrected at α = 0.05, n = 18 control and n = 23 injected, DSL Padj = 3 × 10−5, AS Padj = 0.02). DS1 and DS2 lengths were not significantly different.
