The Hox distal phase/reverse collinear expression pattern is utilized by both the HoxD and HoxA clusters in a variety of distally elongated vertebrate structures. The distal phase (DP) expression pattern occurs with the HoxD genes in the paddlefish barbel (C-D), and with the HoxA genes in the vent of three ray-finned fishes (E-F, I-J, M-R), outlined in black. HoxD12 and HoxD13 are expressed collinearly in the vent (G-H, K-L, not outlined in black), while HoxA11 α, α, is expressed in the barbel (A-B). The stage of peak expression for each gene is shown, but additional time series are shown in Additional files 4, 6-10. The phylogenetic relationships are indicated on the right, with cartoons of overlapping DP expression patterns. The distal phase HoxD expression pattern has previously been shown in the pectoral fins of paddlefish (shown in blue). However, we found that Hox DP expression is manifest with the posterior HoxA genes as well as the HoxD genes, and occurs in a variety of body plan features besides fins and limbs including the paddlefish barbel and vent of ray-finned fishes (shown in red). Teleost fishes (for example, zebrafish and goby) have two HoxA clusters; therefore, we feature expression of the HoxAa and Ab genes when both paralogs are present, and when expression occurs. Zebrafish has only one HoxD cluster, for which the expression patterns are shown. Gobies have two HoxD clusters, but only one D12a gene, and no D13 genes. The paddlefish spiral valve is visible in F-G, and is black in color. In zebrafish, gut development occurs in association with the yolk sac extension (YSE),, a feature that is specific to zebrafish and their relatives, explaining the appearance of compressed expression domains in the hindgut region.