In contrast to all known invertebrates, all vertebrate lineages investigated so far exhibit multiple copies of Hox clusters that presumably arose through genome duplications in early vertebrate evolution and later in the actinopterygian (ray finned fish) lineage [29-33]. These duplication events were followed by massive loss of the duplicated genes in different lineages, see e.g. [34] for a recent review on the situation in teleost fishes. The individual Hox clusters of gnathostomes have a length of some 100,000nt and share besides a set of homologous genes also a substantial amount of conserved non-coding DNA [35] that predominantly consists of transcription factor binding sites. Most recently, however, some of these "phylogenetic footprints" were identified as microRNAs [36].