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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.

Comparative genomics of Lbx loci reveals conservation of identical Lbx ohnologs in bony vertebrates