The study of Hox clusters and genes provides insights into the evolution of 
genomic regulation of development. Derived ray-finned fishes (Actinopterygii, 
Teleostei) such as zebrafish and pufferfish possess duplicated Hox clusters that 
have undergone considerable sequence evolution. Whether these changes are 
associated with the duplication(s) that produced extra Hox clusters is 
unresolved because comparison with basal lineages is unavailable. We sequenced 
and analyzed the HoxA cluster of the bichir (Polypterus senegalus), a 
phylogenetically basal actinopterygian. Independent lines of evidence indicate 
that bichir has one HoxA cluster that is mosaic in its patterns of noncoding 
sequence conservation and gene retention relative to the HoxA clusters of human 
and shark, and the HoxAalpha and HoxAbeta clusters of zebrafish, pufferfish, and 
striped bass. HoxA cluster noncoding sequences conserved between bichir and 
euteleosts indicate that novel cis-sequences were acquired in the stem 
actinopterygians and maintained after cluster duplication. Hence, in the 
earliest actinopterygians, evolution of the single HoxA cluster was already more 
dynamic than in human and shark. This tendency peaked among teleosts after HoxA 
cluster duplication.