Conserved paralogous clusters may result from the initial clustering of the genes in a relatively small ancestral genomic contig. Some evidence for the existence of "protoclusters" that could correspond to the paralogous chromosomal segments noted in higher vertebrates is present in the genome of the urochordate C. intestinalis [11]. For instance, the orthologues of FGFR, and WHSC1, carboxypeptidase Z and FLJ25359 cluster within an 85 kb region of the C. intestinalis genome and the human orthologues are still maintained in paralogous segments of 4p16, 8p and 10q (Fig. 3, [see Additional file 1]). However, it should be noted that no clusters of genes from the vertebrate paralogous segments are locate close to the TACC or RHAMM genes of C. intestinalis, indicating that the formation of the much larger paralogous segments encompassing the FGFR-TACC genes formed later in evolutionary time, or conversely have been subject to extensive rearrangement in tunicates. In combination with the examination of the T. rubripes genome, this also provides additional evidence that either the second round of duplication of the chromosomal segment that contained the FGFR3/4 ancestor did not include a TACC gene, or that such a gene was lost very early in vertebrate evolution, prior to the divergence of the Gnanthostome lineages. However, the final resolution of the initial evolution of these paralogous segment will await the sequencing of the amphioxus and lamprey genomes, which only have one FGFR gene, and therefore should only contain one copy of the other corresponding genes in this conserved segment.