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The role of Homeobox transcription factors during fin and limb development have been the focus of recent work investigating the evolutionary origin of limb-specific morphologies. Here we characterize the expression of  HoxD  genes, as well as the cluster-associated genes  Evx2  and  LNP , in the paddlefish  Polyodon spathula , a basal ray-finned fish. Our results demonstrate a collinear pattern of nesting in early fin buds that includes  HoxD14 , a gene previously thought to be isolated from global  Hox  regulation. We also show that in both  Polyodon  and the catshark  Scyliorhinus canicula  (a representative chondrichthyan) late phase  HoxD  transcripts are present in cells of the fin-fold and co-localize with  And1 , a component of the dermal skeleton. These new data support an ancestral role for  HoxD  genes in patterning the fin-folds of jawed vertebrates, and fuel new hypotheses about the evolution of cluster regulation and the potential downstream differentiation outcomes of distinct  HoxD -regulated compartments.

HoxD expression in the fin-fold compartment of basal gnathostomes and implications for paired appendage evolution