BACKGROUND: Lbx/ladybird genes originated as part of the metazoan cluster of Nk 
homeobox genes. In all animals investigated so far, both the protostome genes 
and the vertebrate Lbx1 genes were found to play crucial roles in neural and 
muscle development. Recently however, additional Lbx genes with divergent 
expression patterns were discovered in amniotes. Early in the evolution of 
vertebrates, two rounds of whole genome duplication are thought to have 
occurred, during which 4 Lbx genes were generated. Which of these genes were 
maintained in extant vertebrates, and how these genes and their functions 
evolved, is not known.
RESULTS: Here we searched vertebrate genomes for Lbx genes and discovered novel 
members of this gene family. We also identified signature genes linked to 
particular Lbx loci and traced the remnants of 4 Lbx paralogons (two of which 
retain Lbx genes) in amniotes. In teleosts, that have undergone an additional 
genome duplication, 8 Lbx paralogons (three of which retain Lbx genes) were 
found. Phylogenetic analyses of Lbx and Lbx-associated genes show that in 
extant, bony vertebrates only Lbx1- and Lbx2-type genes are maintained. Of 
these, some Lbx2 sequences evolved faster and were probably subject to 
neofunctionalisation, while Lbx1 genes may have retained more features of the 
ancestral Lbx gene. Genes at Lbx1 and former Lbx4 loci are more closely related, 
as are genes at Lbx2 and former Lbx3 loci. This suggests that during the second 
vertebrate genome duplication, Lbx1/4 and Lbx2/3 paralogons were generated from 
the duplicated Lbx loci created during the first duplication event.
CONCLUSION: Our study establishes for the first time the evolutionary history of 
Lbx genes in bony vertebrates, including the order of gene duplication events, 
gene loss and phylogenetic relationships. Moreover, we identified genetic 
hallmarks for each of the Lbx paralogons that can be used to trace Lbx genes as 
other vertebrate genomes become available. Significantly, we show that bony 
vertebrates only retained copies of Lbx1 and Lbx2 genes, with some Lbx2 genes 
being highly divergent. Thus, we have established a base on which the evolution 
of Lbx gene function in vertebrate development can be evaluated.