Extended Data Fig. 5: Hox gene expression patterns in Gasterosteus and Apeltes spines and fins.

The expression patterns for each Hox gene in different stickleback Hox clusters are shown with normalized read count on the y-axis and tissue site on the x-axis. The tissues are organized by position from anterior to posterior along the dorsal side of the fish, with the anal fin at the end. The read count shown is the average across all samples for that species; the reads are normalized within each species but not between species. The genes with empty plots exist in both species but are not expressed in the tissues shown with the exception of HOXB6B and HOXB7A, which are located in gaps in the Gasterosteus assembly and thus were not scored; HOXB6B is not expressed in Apeltes, but HOXB7A is expressed. HOXA1A, HOXB1B, and HOXB1B are present in the genomes but were not expressed and are not shown. The genes differentially expressed (padj < 0.01) between the largest anterior spines (DS1 and DS2) in Gasterosteus low-spine (three-spine) fish are HOXA2A, HOXA5A, HOXA10B, HOXC3A, HOXC5A, HOXC9A, HOXC10A, HOXC11A, HOXD3A, HOXD4A, HOXD9A, HOXD10A, HOXD4B, HOXD9B, and HOXD11B; the genes differentially expressed (padj < 0.01) between DS1 and DS3 in Apeltes low-spine (four-spine) fish are HOXA10B, HOXC4A, HOXC8A, HOXC9A, HOXC10A, HOXD9A, HOXD10A, HOXD11A, HOXD4B, HOXD9B, and HOXD11B.